rMSIfragment Figures
This R Markdown was used to generate the figures of the publication of rMSIfragment (DOI). It serves two purposes: (1) Transparency and reproducibility of results (2) Demonstration of the main applications of rMSIfragment (for a more detailed demonstration explore demo.Rmd)
Load dependencies
library(rMSI)
library(rMSIproc)
library(rMSIfragment)
library(ggplot2)
library(viridisLite)0.1. Load data
0.2. Annotate in-source fragments and adducts
Figure 1. Manual Validation (Negative mode 5 ppm)
rMSIfragment:::plot_figure1(res.neg.5ppm.td1,metrics[1:3],label="_NEG_D1_N")Warning in grDevices::dev.off() :
unable to open TIFF file '/home/gbaquer/msidata/1. In-source Fragmentation/1.6. Paper/Figures//Fig1_Target_Decoy_Validation_NEG_D1_N.tiff'
rMSIfragment:::plot_figure2(pks_neg,res.neg.5ppm,gt_neg,"S",steps = 1000,label="_adduct_score")Warning in grDevices::dev.off() :
unable to open TIFF file '/home/gbaquer/msidata/1. In-source Fragmentation/1.6. Paper/Figures//Fig2_Manual_Validation_adduct_score.tiff'
rMSIfragment:::plot_figure3(pks_neg,res.neg.5ppm,744.558,3,label="_5ppm_top3")Warning: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.
Warning: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.
Warning: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.
Warning: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.
Scale for 'colour' is already present. Adding another scale for 'colour', which will replace the existing scale.
Warning in grDevices::dev.off() :
unable to open TIFF file '/home/gbaquer/msidata/1. In-source Fragmentation/1.6. Paper/Figures//Fig3_Example_Annotations_5ppm_top3.tiff'
rMSIfragment:::plot_figure1(res.neg.5ppm.td2,metrics[1:3],label="_NEG_D1_N")Warning in grDevices::dev.off() :
unable to open TIFF file '/home/gbaquer/msidata/1. In-source Fragmentation/1.6. Paper/Figures//Fig1_Target_Decoy_Validation_NEG_D1_N.tiff'
rMSIfragment:::plot_figure2(pks_neg,res.neg.20ppm,gt_neg,"S",steps = 1000,label="_adduct_score")Warning in grDevices::dev.off() :
unable to open TIFF file '/home/gbaquer/msidata/1. In-source Fragmentation/1.6. Paper/Figures//Fig2_Manual_Validation_adduct_score.tiff'
rMSIfragment:::plot_figure3(pks_neg,res.neg.20ppm,744.558,3,label="_5ppm_top3")Warning: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.
Warning: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.
Warning: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.
Warning: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.
Scale for 'colour' is already present. Adding another scale for 'colour', which will replace the existing scale.
Warning in grDevices::dev.off() :
unable to open TIFF file '/home/gbaquer/msidata/1. In-source Fragmentation/1.6. Paper/Figures//Fig3_Example_Annotations_5ppm_top3.tiff'
Check separation between parental vs fragment
#Compute parental
tmp<-rMSIfragment:::manual_validation(res.neg.20ppm,gt_neg)
t<-tmp$table
a<-subset(d$adducts,mode=="neg")$name
t$parental<-t$adduct%in%a
subset(t,!match&HPLC_adduct!="_")
#Quantify score for HPLC
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[ reached getOption("max.print") -- omitted 8407 entries ]i<-tmp$res$match_HPLC_adduct!=""
pval<-mean(sapply(1:100,function(j)wilcox.test(sample(tmp$res$S[!i],sum(i)), tmp$res$S[i], alternative = "two.sided")$p.value))
PR curve
#roc<-td_roc(tmp$res$S,i,mz_i)
#auc<-mean(sapply(1:500,function(j)PRROC::pr.curve(scores.class1 = sample(tmp$res$S[!i],sum(i)),scores.class0=tmp$res$S[i],curve=T)$auc.integral))
pr<-PRROC::pr.curve(scores.class1 = tmp$res$S[i],scores.class0=tmp$res$S[!i],curve=T)
df<-data.frame(x=pr$curve[,1],y=pr$curve[,2])
pb<-ggplot(df,aes(x,y))+geom_line(size=2)+
xlab("Recall")+ylab("Precision")+
theme_bw()+theme(legend.justification = c(1, 0), legend.position = c(1, 0),legend.background=element_rect(size=0.2,colour=1),panel.border = element_rect(colour = "black", fill=NA), panel.grid.major = element_blank(),
panel.grid.minor = element_blank(), plot.title = element_text(hjust = 0),text=element_text(size=20)) +
ggtitle("B")#+
#scale_color_discrete(name = "Score", breaks = names,labels = paste(names," (",round(pr$auc.integral,2)," AUC)",sep = ""))
pb
pr$auc.integral
rcFinal$curve<-
rc<-PRROC::roc.curve(scores.class0 = tmp$res$S[i],scores.class1=sample(tmp$res$S[!i],sum(i)),curve=T)
df<-data.frame(x=rc$curve[,1],y=rc$curve[,2])
pc<-ggplot(df,aes(x,y))+geom_line(size=2)+
xlab("False Positive Rate")+ylab("Sensitivity")+
theme_bw()+theme(legend.justification = c(1, 0), legend.position = c(1, 0),legend.background=element_rect(size=0.2,colour=1),panel.border = element_rect(colour = "black", fill=NA), panel.grid.major = element_blank(),
panel.grid.minor = element_blank(), plot.title = element_text(hjust = 0),text=element_text(size=20)) +
ggtitle("c")#+
#scale_color_discrete(name = "Score", breaks = names,labels = paste(names," (",round(pr$auc.integral,2)," AUC)",sep = ""))
pc
rc$auc###
rc2<-lapply(1:1000,function(j)PRROC::roc.curve(scores.class0 = tmp$res$S[i],scores.class1=sample(tmp$res$S[!i],sum(i)),curve=T))
df<-data.frame(x=unlist(lapply(rc2,function(x)x$curve[,1])),y=unlist(lapply(rc2,function(x)x$curve[,2])),id=rep(1:length(rc2),times=sapply(rc2,function(x)length(x$curve[,1]))))
ggplot(df, aes(x = x, y = y)) +
geom_line(aes(group = id), alpha = 0.5) +
geom_smooth(size = 0.8, se = F, span = 0.2)`geom_smooth()` using method = 'gam' and formula 'y ~ s(x, bs = "cs")'
#rMSIfragment:::plot_figure1(res.pos.5ppm.td1,metrics[1:3],label="_NEG_D1_N")
rMSIfragment:::plot_figure2(pks_pos,res.pos.5ppm,gt_pos,"S",steps = 1000,label="_adduct_score")Warning in grDevices::dev.off() :
unable to open TIFF file '/home/gbaquer/msidata/1. In-source Fragmentation/1.6. Paper/Figures//Fig2_Manual_Validation_adduct_score.tiff'
#rMSIfragment:::plot_figure3(pks_pos,res.pos.5ppm,744.558,3,label="_5ppm_top3")
#rMSIfragment:::plot_figure1(res.pos.5ppm.td2,metrics[1:3],label="_NEG_D1_N")
rMSIfragment:::plot_figure2(pks_pos,res.pos.20ppm,gt_pos,"S",steps = 1000,label="_adduct_score")Warning in grDevices::dev.off() :
unable to open TIFF file '/home/gbaquer/msidata/1. In-source Fragmentation/1.6. Paper/Figures//Fig2_Manual_Validation_adduct_score.tiff'
#rMSIfragment:::plot_figure3(pks_pos,res.pos.20ppm,744.558,3,label="_5ppm_top3")Figure 1. Manual Validation (Negative mode 20 ppm)
rMSIfragment:::plot_figure1(res1,metrics,label="_NEG_D1_N")
rMSIfragment:::plot_figure2(pks_neg,res,gt_neg,"adduct_score",label="_adduct_score")
rMSIfragment:::plot_figure3(pks_neg,res,744.558,3,label="_5ppm_top3")Figure 2. Target Decoy Validation
Figure 3. METASPACE Validation (They use 3ppm tolerance)
files=list.files(path = "E:/in-source fragmentation/METASPACE/",pattern = "*.zip", full.names = TRUE,recursive = T)
pks_MS<-lapply(files,rMSIproc::LoadPeakMatrix)
csvfiles=gsub(".zip",".csv",files)
ann_MS<-lapply(csvfiles,function(x)read.csv(x,skip=2))
df<-data.frame(name=basename(files))
df$mode<-sapply(strsplit(basename(files),"_"),function(x)tolower(x[1]))
df$matrix<-sapply(strsplit(basename(files),"_"),function(x)tolower(x[2]))
df$specimen<-sapply(strsplit(basename(files),"_"),function(x)tolower(x[3]))
df$tissue<-sapply(strsplit(basename(files),"_"),function(x)tolower(x[4]))
df$analyzer<-sapply(strsplit(basename(files),"_"),function(x)tolower(x[4]))
df$mz.mean<-sapply(pks_MS,function(x)mean(x$mass))
df$mz.max<-sapply(pks_MS,function(x)max(x$mass))
df$mz.min<-sapply(pks_MS,function(x)min(x$mass))Annotate with rMSIfragment
res_MS<-lapply(seq_along(pks_MS),function(i)rMSIfragment::annotate(pks_MS[[i]],new,3,df$mode[i]))rbind(sapply(res_MS,nrow),sapply(ann_MS,nrow),sapply(pks_MS,function(x)min(x$mass)),sapply(pks_MS,function(x)max(x$mass))) [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13] [,14] [,15] [,16]
[1,] 237.0000 205.0000 27.0000 10021.0000 420.0000 2612.0000 596.0000 247258.0000 121.0000 2503.000 1248.0000 2203.0000 3107.0000 2406.0000 3390.0000 97.00000
[2,] 407.0000 344.0000 131.0000 319.0000 790.0000 649.0000 167.0000 889.0000 121.0000 276.000 831.0000 870.0000 2391.0000 2320.0000 3448.0000 912.00000
[3,] 202.0393 201.0242 215.0362 182.0484 299.8179 401.0702 402.7255 180.0697 206.0553 313.028 104.3449 259.1606 312.9989 365.8185 400.3417 70.06599
[4,] 887.7977 529.3906 885.8488 1903.9571 1366.2796 943.5830 1644.5788 1812.0428 783.2954 1463.211 851.8328 1281.9519 1293.2040 1293.0984 1590.7703 390.94544Compare the results
i<-10
compareToMetaspace<-function(ours,metaspace,pks){
a1<-ours
a2<-subset(a1,fragmentation=="")
a3<-subset(a1,fragmentation!="")
b<-metaspace
b$mz_i<-sapply(b$mz,function(x) which.min(abs(pks$mass-x)))
matching<-paste(b$formula,b$adduct)%in%paste(a2$formula,a2$adduct)
overlappedWithFragments<-paste(b$mz_i)%in%paste(a3$mz_i)
compoundsWithFragments<-b$formula%in%a3$formula
covered<-b$formula%in%new$formula
print(nrow(ours))
return(list(covered=sum(covered)/nrow(b),matching=sum(matching)/nrow(b),overlappedWithFragments=sum(overlappedWithFragments)/nrow(b),compoundsWithFragments=sum(compoundsWithFragments)/nrow(b),v.matching=matching,v.overlappedWithFragments=overlappedWithFragments,v.compoundsWithFragments=compoundsWithFragments))
}
comp<-lapply(seq_along(pks_MS),function(i)compareToMetaspace(res_MS[[i]],ann_MS[[i]],pks_MS[[i]]))[1] 237
[1] 205
[1] 27
[1] 10021
[1] 420
[1] 2612
[1] 596
[1] 247258
[1] 121
[1] 2503
[1] 1248
[1] 2203
[1] 3107
[1] 2406
[1] 3390
[1] 97df$covered<-sapply(comp,function(x)x$covered)
df$matching<-sapply(comp,function(x)x$matching)
df$overlappedWithFragments<-sapply(comp,function(x)x$overlappedWithFragments)
df$compoundsWithFragments<-sapply(comp,function(x)x$compoundsWithFragments)
ggplot(df,aes(x=matching,y=covered,label=1:16))+geom_point()+geom_text(hjust=0,vjust=0)
Figure 4. Example application
pks_MUN<-rMSIproc::LoadPeakMatrix("E:/in-source fragmentation/MUNSTER/Munster_Au_Res_140k_10um.zip")rMSIproc::plotPeakImage(pks_MUN,column=1000)Updating the databases
new<-rMSIfragment:::load_lipidMAPS("E:/in-source fragmentation/DATA/db/LMSD.sdf")
old<-rMSIfragment:::load_lipidMAPS("E:/in-source fragmentation/DATA/db/LMSDold.sdf")
tmp<-rMSIfragment:::load_decoy_non_animal(NA,"E:/in-source fragmentation/DATA/chebi/")
plot(density(tmp$exactmass))
lines(density(db_t$exactmass))
tmp2<-rMSIfragment:::adjust_db_densities(db_t,tmp)
lines(density(tmp2$exactmass))
db_d<-tmp2
save(list=c("db_t","db_d"),file="E:/in-source fragmentation/DATA/target_decoy_db_new.RData")Move to figure generation new Use either 4, 6 or 8
lapply(pks_MS,function(x)rMSIproc::plotPeakImage(x,column=900))Warning in max(unlist(lapply(lstRefac[ind_offsets], function(x) { :
no non-missing arguments to max; returning -Inf
Warning in max(unlist(lapply(lstRefac[ind_offsets], function(x) { :
no non-missing arguments to max; returning -Inf
Warning in max(unlist(lapply(lstRefac[ind_offsets], function(x) { :
no non-missing arguments to max; returning -Inf
Warning in max(unlist(lapply(lstRefac[ind_offsets], function(x) { :
no non-missing arguments to max; returning -Inf
Warning in max(unlist(lapply(lstRefac[ind_offsets], function(x) { :
no non-missing arguments to max; returning -Inf
Warning in max(unlist(lapply(lstRefac[ind_offsets], function(x) { :
no non-missing arguments to max; returning -Inf
Warning in max(unlist(lapply(lstRefac[ind_offsets], function(x) { :
no non-missing arguments to max; returning -Inf
Warning in max(unlist(lapply(lstRefac[ind_offsets], function(x) { :
no non-missing arguments to max; returning -Inf
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Using 4
1
[1] 1matched_us<-matched_us[order(matched_us$S),]
matched_us<-matched_us[order(matched_us$S),]rMSIfragment:::plot_figure3(pks_MS[[4]],res_MS[[4]],772.5864,3,label="_5ppm_top3")Warning: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.
Warning: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.
Warning: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.
Warning: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.
Scale for 'colour' is already present. Adding another scale for 'colour', which will replace the existing scale.
Warning in grDevices::dev.off() :
unable to open TIFF file '/home/gbaquer/msidata/1. In-source Fragmentation/1.6. Paper/Figures//Fig3_Example_Annotations_5ppm_top3.tiff'
rMSIfragment:::plot_figure3(pks_MS[[4]],res_MS[[4]],744.5553,3,label="_5ppm_top3")Warning: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.
Warning: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.
Warning: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.
Warning: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.
Scale for 'colour' is already present. Adding another scale for 'colour', which will replace the existing scale.
Warning in grDevices::dev.off() :
unable to open TIFF file '/home/gbaquer/msidata/1. In-source Fragmentation/1.6. Paper/Figures//Fig3_Example_Annotations_5ppm_top3.tiff'
rMSIfragment:::plot_figure3(pks_MS[[4]],res_MS[[4]],887.5661,3,label="_5ppm_top3")Warning: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.
Warning: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.
Warning: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.
Warning: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.
Scale for 'colour' is already present. Adding another scale for 'colour', which will replace the existing scale.
Warning in grDevices::dev.off() :
unable to open TIFF file '/home/gbaquer/msidata/1. In-source Fragmentation/1.6. Paper/Figures//Fig3_Example_Annotations_5ppm_top3.tiff'
rMSIfragment:::plot_figure3(pks_MS[[4]],res_MS[[4]],788.5452,3,label="_5ppm_top3")Warning: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.
Warning: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.
Warning: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.
Warning: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.
Scale for 'colour' is already present. Adding another scale for 'colour', which will replace the existing scale.
Warning in grDevices::dev.off() :
unable to open TIFF file '/home/gbaquer/msidata/1. In-source Fragmentation/1.6. Paper/Figures//Fig3_Example_Annotations_5ppm_top3.tiff'
them[which.min(abs(them$mz-887.57)),]
them[which.min(abs(them$mz-836.53)),]
them[which.min(abs(them$mz-749.51)),]Reprocess all datasets
files_imzML=list.files(path = "E:/in-source fragmentation/METASPACE/new3/",pattern = "*.imzML", full.names = TRUE,recursive = T)
files_zip=gsub("*.imzML",".zip",files_imzML)
for(i in seq_along(files_imzML)){
tmp<-rMSIworkflows:::loadBinnedCentroidData(files_imzML[i],3)
rMSIproc::StorePeakMatrix(files_zip[i],tmp)
}